1. science
2. mathematics
3. statistics

A Kernel Method for the Two-Sample-Problem
Arthur Gretton
MPI for Biological Cybernetics
T¨ubingen, Germany
[email protected]
Karsten M. Borgwardt
Ludwig-Maximilians-Univ.
Munich, Germany
[email protected]
Bernhard Sch¨olkopf
MPI for Biological Cybernetics
T¨ubingen, Germany
[email protected]
Malte Rasch
Graz Univ. of Technology,
Graz, Austria
[email protected]
Alexander J. Smola
NICTA, ANU
Canberra, Australia
[email protected]
Abstract
We propose two statistical tests to determine if two samples are from different distributions. Our test statistic is in both cases the distance between the means of the
two samples mapped into a reproducing kernel Hilbert space (RKHS). The first
test is based on a large deviation bound for the test statistic, while the second is
based on the asymptotic distribution of this statistic. The test statistic can be computed in O(m2 ) time. We apply our approach to a variety of problems, including
attribute matching for databases using the Hungarian marriage method, where our
test performs strongly. We also demonstrate excellent performance when comparing distributions over graphs, for which no alternative tests currently exist.
1 Introduction
We address the problem of comparing samples from two probability distributions, by proposing a
statistical test of the hypothesis that these distributions are different (this is called the two-sample
or homogeneity problem). This test has application in a variety of areas. In bioinformatics, it is
of interest to compare microarray data from different tissue types, either to determine whether two
subtypes of cancer may be treated as statistically indistinguishable from a diagnosis perspective,
or to detect differences in healthy and cancerous tissue. In database attribute matching, it is desirable to merge databases containing multiple fields, where it is not known in advance which fields
correspond: the fields are matched by maximising the similarity in the distributions of their entries.
In this study, we propose to test whether distributions p and q are different on the basis of samples
drawn from each of them, by finding a smooth function which is large on the points drawn from p,
and small (as negative as possible) on the points from q. We use as our test statistic the difference
between the mean function values on the two samples; when this is large, the samples are likely
from different distributions. We call this statistic the Maximum Mean Discrepancy (MMD).
Clearly the quality of MMD as a statistic depends heavily on the class F of smooth functions that
define it. On one hand, F must be “rich enough” so that the population MMD vanishes if and only
if p = q. On the other hand, for the test to be consistent, F needs to be “restrictive” enough for the
empirical estimate of MMD to converge quickly to its expectation as the sample size increases. We
shall use the unit balls in universal reproducing kernel Hilbert spaces [22] as our function class, since
these will be shown to satisfy both of the foregoing properties. On a more practical note, MMD is
cheap to compute: given m points sampled from p and n from q, the cost is O(m + n)2 time.
We define two non-parametric statistical tests based on MMD. The first, which uses distributionindependent uniform convergence bounds, provides finite sample guarantees of test performance,
at the expense of being conservative in detecting differences between p and q. The second test is
based on the asymptotic distribution of MMD, and is in practice more sensitive to differences in
distribution at small sample sizes. These results build on our earlier work in [6] on MMD for the
two sample problem, which addresses only the second kind of test. In addition, the present approach
employs a more accurate approximation to the asymptotic distribution of the test statistic.
We begin our presentation in Section 2 with a formal definition of the MMD, and a proof that the
population MMD is zero if and only if p = q when F is the unit ball of a universal RKHS. We also
give an overview of hypothesis testing as it applies to the two-sample problem, and review previous
approaches. In Section 3, we provide a bound on the deviation between the population and empirical
MMD, as a function of the Rademacher averages of F with respect to p and q. This leads to a first
hypothesis test. We take a different approach in Section 4, where we use the asymptotic distribution
of an unbiased estimate of the squared MMD as the basis for a second test. Finally, in Section 5, we
demonstrate the performance of our method on problems from neuroscience, bioinformatics, and
attribute matching using the Hungarian marriage approach. Our approach performs well on high
dimensional data with low sample size; in addition, we are able to successfully apply our test to
graph data, for which no alternative tests exist. Proofs and further details are provided in [13].
2 The Two-Sample-Problem
Our goal is to formulate a statistical test that answers the following question:
Problem 1 Let p and q be distributions defined on a domain X. Given observations X :=
{x1 , . . . , xm } and Y := {y1 , . . . , yn }, drawn independently and identically distributed (i.i.d.) from
p and q respectively, is p 6= q?
To start with, we wish to determine a criterion that, in the population setting, takes on a unique and
distinctive value only when p = q. It will be defined based on [10, Lemma 9.3.2].
Lemma 1 Let (X, d) be a separable metric space, and let p, q be two Borel probability measures
defined on X. Then p = q if and only if Ep (f (x)) = Eq (f (x)) for all f ∈ C(X), where C(X) is the
space of continuous bounded functions on X.
Although C(X) in principle allows us to identify p = q uniquely, it is not practical to work with such
a rich function class in the finite sample setting. We thus define a more general class of statistic, for
as yet unspecified function classes F, to measure the discrepancy between p and q, as proposed in
[11].
Definition 2 Let F be a class of functions f : X → R and let p, q, X, Y be defined as above. Then
we define the maximum mean discrepancy (MMD) and its empirical estimate as
MMD [F, p, q] := sup (Ex∼p [f (x)] − Ey∼q [f (y)]) ,
(1)
f ∈F
MMD [F, X, Y ] := sup
f ∈F
!
m
n
1 X
1X
f (xi ) −
f (yi ) .
m i=1
n i=1
(2)
We must now identify a function class that is rich enough to uniquely establish whether p = q, yet
restrictive enough to provide useful finite sample estimates (the latter property will be established
in subsequent sections). To this end, we select F to be the unit ball in a universal RKHS H [22];
we will henceforth use F only to denote this function class. With the additional restriction that X be
compact, a universal RKHS is dense in C(X) with respect to the L∞ norm. It is shown in [22] that
Gaussian and Laplace kernels are universal.
Theorem 3 Let F be a unit ball in a universal RKHS H, defined on the compact metric space X,
with associated kernel k(·, ·). Then MMD [F, p, q] = 0 if and only if p = q.
This theorem is proved in [13]. We next express the MMD in a more easily computable form. This
is simplified by the fact that in an RKHS, function evaluations can be written f (x) = hφ(x), f i,
where φ(x) = k(x, .). Denote by µ[p] := Ex∼p(x) [φ(x)] the expectation of φ(x) (assuming that it
exists).1 Since Ep [f (x)] = hµ[p], f i, we may rewrite
MMD[F, p, q] = sup hµ[p] − µ[q], f i = kµ[p] − µ[q]kH .
(3)
kf kH ≤1
1
m
Pm
φ(xi ) and k(x, x0 ) = hφ(x), φ(x0 )i, an empirical estimate of MMD is
 21

m,n
m
n
X
X
X
1
2
1
k(xi , yj ) + 2
k(xi , xj ) −
k(yi , yj ) . (4)
MMD [F, X, Y ] =  2
m i,j=1
mn i,j=1
n i,j=1
Using µ[X] :=
i=1
Eq. (4) provides us with a test statistic for p 6= q. We shall see in Section 3 that this estimate is
biased, although it is straightforward to upper bound the bias (we give an unbiased estimate, and an
associated test, in Section 4). Intuitively we expect MMD[F, X, Y ] to be small if p = q, and the
quantity to be large if the distributions are far apart. Note that it costs O((m + n)2 ) time to compute
the statistic.
Overview of Statistical Hypothesis Testing, and of Previous Approaches Having defined our
test statistic, we briefly describe the framework of statistical hypothesis testing as it applies in the
present context, following [9, Chapter 8]. Given i.i.d. samples X ∼ p of size m and Y ∼ q of
size n, the statistical test, T(X, Y ) : Xm × Xn 7→ {0, 1} is used to distinguish between the null
hypothesis H0 : p = q and the alternative hypothesis H1 : p 6= q. This is achieved by comparing
the test statistic MMD[F, X, Y ] with a particular threshold: if the threshold is exceeded, then the
test rejects the null hypothesis (bearing in mind that a zero population MMD indicates p = q). The
acceptance region of the test is thus defined as any real number below the threshold. Since the test is
based on finite samples, it is possible that an incorrect answer will be returned: we define the Type I
error as the probability of rejecting p = q based on the observed sample, despite the null hypothesis
being true. Conversely, the Type II error is the probability of accepting p = q despite the underlying
distributions being different. The level α of a test is an upper bound on the Type I error: this is a
design parameter of the test, and is used to set the threshold to which we compare the test statistic
(finding the test threshold for a given α is the topic of Sections 3 and 4). A consistent test achieves
a level α, and a Type II error of zero, in the large sample limit. We will see that both of the tests
proposed in this paper are consistent.
We next give a brief overview of previous approaches to the two sample problem for multivariate
data. Since our later experimental comparison is with respect to certain of these methods, we give
abbreviated algorithm names in italics where appropriate: these should be used as a key to the
tables in Section 5. We provide further details in [13]. A generalisation of the Wald-Wolfowitz
runs test to the multivariate domain was proposed and analysed in [12, 17] (Wolf), which involves
counting the number of edges in the minimum spanning tree over the aggregated data that connect
points in X to points in Y . The computational cost of this method using Kruskal’s algorithm is
O((m + n)2 log(m + n)), although more modern methods improve on the log(m + n) term. Two
possible generalisations of the Kolmogorov-Smirnov test to the multivariate case were studied in
[4, 12]. The approach of Friedman and Rafsky (Smir) in this case again requires a minimal spanning
tree, and has a similar cost to their multivariate runs test. A more recent multivariate test was
proposed in [20], which is based on the minimum distance non-bipartite matching over the aggregate
data, at cost O((m + n)3 ). Another recent test was proposed in [15] (Hall): for each point from
p, it requires computing the closest points in the aggregated data, and counting how many of these
are from q (the procedure is repeated for each point from q with respect to points from p). The test
statistic is costly to compute; [15] consider only tens of points in their experiments.
Yet another approach is to use some distance (e.g. L1 or L2 ) between Parzen window estimates
of the densities as a test statistic [1, 3], based on the asymptotic distribution of this distance given
p = q. When the L2 norm is used, the test statistic is related to those we present here, although it
is arrived at from a different perspective (see [13]: the Parzen window interpretation is problematic,
since the resulting two-sample test is not consistent when the kernel size is decreased fast enough to
ensure a consistent Parzen window estimate). The L1 approach of [3] (Biau) requires the space to be
partitioned into a grid of bins, which becomes difficult or impossible for high dimensional problems.
Hence we use this test only for low-dimensional problems in our experiments.
1
A sufficient condition for this is kµ[p]k2H < ∞, which is rearranged as Ep [k(x, x0 )] < ∞, where x and
x0 are independent random variables drawn according to p.
3 A Test based on Uniform Convergence Bounds
In this section, we establish two properties of the MMD. First, we show
√ that regardless of whether or
not p = q, the empirical MMD converges in probability at rate 1/ m + n to its population value.
This establishes the consistency of statistical tests based on MMD. Second, we give probabilistic
bounds for large deviations of the empirical MMD in the case p = q. These bounds lead directly to
a threshold for our first hypothesis test.
We begin our discussion of the convergence of MMD[F, X, Y ] to MMD[F, p, q].
Theorem 4 Let p, q, X, Y be defined as in Problem 1, and assume |k(x, y)| ≤ K. Then
n
o
1
1
−2 mn
Pr |MMD[F, X, Y ] − MMD[F, p, q]| > 2 (K/m) 2 + (K/n) 2 + ≤ 2 exp 2K(m+n)
.
Our next goal is to refine this result in a way that allows us to define a test threshold under the null
hypothesis p = q. Under this circumstance, the constants in the exponent are slightly improved.
Theorem 5 Under the conditions of Theorem 4 where additionally p = q and m = n,
q
1
MMD[F, X, Y ] > m− 2 2Ep [k(x, x) − k(x, x0 )] + > 2(K/m)1/2 + ,
| {z }
|
{z
}
B2 (F,p)
B1 (F,p)
2 m
(see [13] for the proof).
both with probability less than exp − 4K
In this theorem, we illustrate two possible bounds B1 (F, p) and B2 (F, p) on the bias in the empirical
estimate (4). The first inequality is interesting inasmuch as it provides a link between the bias bound
B1 (F, p) and kernel size (for instance, if we were to use a Gaussian kernel with large σ, then k(x, x)
and k(x, x0 ) would likely be close, and the bias small). In the context of testing, however, we would
need to provide an additional bound to show convergence of an empirical estimate of B1 (F, p) to its
population equivalent. Thus, in the following test for p = q based on Theorem 5, we use B2 (F, p)
to bound the bias.
Lemma 6 A hypothesis test of level α for the null hypothesis
q (equivalently
MMD[F, p, q] =
p=
p
p
−1
0) has the acceptance region MMD[F, X, Y ] < 2 K/m 1 + log α
.
We emphasise that Theorem 4 guarantees
√ the consistency of the test, and that the Type II error
probability decreases to zero at rate 1/ m (assuming m = n). To put this convergence rate in
perspective, consider a test of whether two normal distributions have equal means, given they have
unknown but equal variance [9, Exercise 8.41]. In this case, the test statistic has a Student-t distribution with n + m − 2 degrees of freedom, and its error probability converges at the same rate as
our test.
4 An Unbiased Test Based on the Asymptotic Distribution of the U-Statistic
We now propose a second test, which is based on the asymptotic distribution of an unbiased estimate
of MMD2 . We begin by defining this test statistic.
Lemma 7 Given x and x0 independent random variables with distribution p, and y and y 0 independent random variables with distribution q, the population MMD2 is
MMD2 [F, p, q] = Ex,x0 ∼p [k(x, x0 )] − 2Ex∼p,y∼q [k(x, y)] + Ey,y0 ∼q [k(y, y 0 )]
(5)
(see [13] for details). Let Z := (z1 , . . . , zm ) be m i.i.d. random variables, where zi := (xi , yi ) (i.e.
we assume m = n). An unbiased empirical estimate of MMD2 is
m
X
1
2
MMDu [F, X, Y ] =
h(zi , zj ),
(6)
(m)(m − 1)
i6=j
which is a one-sample U-statistic with h(zi , zj ) := k(xi , xj ) + k(yi , yj ) − k(xi , yj ) − k(xj , yi ).
The empirical statistic is an unbiased estimate of MMD2 , although it does not have minimum variance (the minimum variance estimate is almost identical: see [21, Section 5.1.4]). We remark that
these quantities can easily be linked with a simple kernel between probability measures: (5) is a
special case of the Hilbertian metric [16, Eq. (4)] with the associated kernel K(p, q) = Ep,q k(x, y)
[16, Theorem 4]. The asymptotic distribution of this test statistic under H1 is given by [21, Section
5.5.1], and the distribution under H0 is computed based on [21, Section 5.5.2] and [1, Appendix];
see [13] for details.
Theorem 8 We assume E h2 < ∞. Under H1 , MMD2u converges in distribution (defined e.g. in
[14, Section 7.2]) to a Gaussian according to
D
1
m 2 MMD2u − MMD2 [F, p, q] → N 0, σu2 ,
√
2
where σu2 = 4 Ez (Ez0 h(z, z 0 ))2 − [Ez,z0 (h(z, z 0 ))] , uniformly at rate 1/ m [21, Theorem
B, p. 193]. Under H0 , the U-statistic is degenerate, meaning Ez0 h(z, z 0 ) = 0. In this case, MMD2u
converges in distribution according to
D
mMMD2u →
∞
X
l=1
λl zl2 − 2 ,
(7)
where zl ∼ N(0, 2) i.i.d., λi are the solutions to the eigenvalue equation
Z
˜ x0 )ψi (x)dp(x) = λi ψi (x0 ),
k(x,
X
˜ i , xj ) := k(xi , xj ) − Ex k(xi , x) − Ex k(x, xj ) + Ex,x0 k(x, x0 ) is the centred RKHS kernel.
and k(x
Our goal is to determine whether the empirical test statistic MMD2u is so large as to be outside the
1 − α quantile of the null distribution in (7) (consistency of the resulting test is guaranteed by the
form of the distribution under H1 ). One way to estimate this quantile is using the bootstrap [2] on the
aggregated data. Alternatively, we may approximate the null distribution by fitting Pearson curves
to its first four moments [18, Section 18.8]. Taking advantage of the degeneracy of the U-statistic,
we obtain (see [13])
2 2
Ez,z0 h2 (z, z 0 )
=
E MMD2u
m(m − 1)
and
3 8(m − 2)
(8)
Ez,z0 [h(z, z 0 )Ez00 (h(z, z 00 )h(z 0 , z 00 ))] + O(m−4 ).
= 2
E MMD2u
m (m − 1)2
4 is not computed, since it is both very small (O(m−4 ))
The fourth moment E MMD2u
and expensive to calculate (O(m4 )). Instead, we replace the kurtosis with its lower bound
2
+ 1.
kurt MMD2u ≥ skew MMD2u
5 Experiments
We conducted distribution comparisons using our MMD-based tests on datasets from three realworld domains: database applications, bioinformatics, and neurobiology. We investigated the
uniform convergence approach (MMD), the asymptotic approach with bootstrap (MMD2u B),
and the asymptotic approach with moment matching to Pearson curves (MMD2u M). We also
compared against several alternatives from the literature (where applicable): the multivariate ttest, the Friedman-Rafsky Kolmogorov-Smirnov generalisation (Smir), the Friedman-Rafsky WaldWolfowitz generalisation (Wolf), the Biau-Gy¨orfi test (Biau), and the Hall-Tajvidi test (Hall). Note
that we do not apply the Biau-Gy¨orfi test to high-dimensional problems (see end of Section 2), and
that MMD is the only method applicable to structured data such as graphs.
An important issue in the practical application of the MMD-based tests is the selection of the kernel
parameters. We illustrate this with a Gaussian RBF kernel, where we must choose the kernel width
σ (we use this kernel for univariate and multivariate data, but not for graphs). The empirical MMD is
zero both for kernel size σ = 0 (where the aggregate Gram matrix over X and Y is a unit matrix), and
also approaches zero as σ → ∞ (where the aggregate Gram matrix becomes uniformly constant).
We set σ to be the median distance between points in the aggregate sample, as a compromise between
these two extremes: this remains a heuristic, however, and the optimum choice of kernel size is an
ongoing area of research.
Data integration As a first application of MMD, we performed distribution testing for data integration: the objective is to aggregate two datasets into a single sample, with the understanding that
both original samples are generated from the same distribution. Clearly, it is important to check
this last condition before proceeding, or an analysis could detect patterns in the new dataset that are
caused by combining the two different source distributions, and not by real-world phenomena. We
chose several real-world settings to perform this task: we compared microarray data from normal
and tumor tissues (Health status), microarray data from different subtypes of cancer (Subtype), and
local field potential (LFP) electrode recordings from the Macaque primary visual cortex (V1) with
and without spike events (Neural Data I and II). In all cases, the two data sets have different statistical
properties, but the detection of these differences is made difficult by the high data dimensionality.
We applied our tests to these datasets in the following fashion. Given two datasets A and B, we either
chose one sample from A and the other from B (attributes = different); or both samples from either
A or B (attributes = same). We then repeated this process up to 1200 times. Results are reported
in Table 1. Our asymptotic tests perform better than all competitors besides Wolf: in the latter case,
we have greater Type II error for one neural dataset, lower Type II error on the Health Status data
(which has very high dimension and low sample size), and identical (error-free) performance on the
remaining examples. We note that the Type I error of the bootstrap test on the Subtype dataset is far
from its design value of 0.05, indicating that the Pearson curves provide a better threshold estimate
for these low sample sizes. For the remaining datasets, the Type I errors of the Pearson and Bootstrap
approximations are close. Thus, for larger datasets, the bootstrap is to be preferred, since it costs
O(m2 ), compared with a cost of O(m3 ) for Pearson (due to the cost of computing (8)). Finally, the
uniform convergence-based test is too conservative, finding differences in distribution only for the
data with largest sample size.
Dataset
Neural Data I
Neural Data II
Health status
Subtype
Attr.
Same
Different
Same
Different
Same
Different
Same
Different
MMD
100.0
50.0
100.0
100.0
100.0
100.0
100.0
100.0
MMD2u B
96.5
0.0
94.6
3.3
95.5
1.0
99.1
0.0
MMD2u M
96.5
0.0
95.2
3.4
94.4
0.8
96.4
0.0
t-test
100.0
42.0
100.0
100.0
100.0
100.0
100.0
100.0
Wolf
97.0
0.0
95.0
0.8
94.7
2.8
94.6
0.0
Smir
95.0
10.0
94.5
31.8
96.1
44.0
97.3
28.4
Hall
96.0
49.0
96.0
5.9
95.6
35.7
96.5
0.2
Table 1: Distribution testing for data integration on multivariate data. Numbers indicate the percentage of repetitions for which the null hypothesis (p=q) was accepted, given α = 0.05. Sample
size (dimension; repetitions of experiment): Neural I 4000 (63; 100) ; Neural II 1000 (100; 1200);
Health Status 25 (12,600; 1000); Subtype 25 (2,118; 1000).
Attribute matching Our second series of experiments addresses automatic attribute matching.
Given two databases, we want to detect corresponding attributes in the schemas of these databases,
based on their data-content (as a simple example, two databases might have respective fields Wage
and Salary, which are assumed to be observed via a subsampling of a particular population, and we
wish to automatically determine that both Wage and Salary denote to the same underlying attribute).
We use a two-sample test on pairs of attributes from two databases to find corresponding pairs.2 This
procedure is also called table matching for tables from different databases. We performed attribute
matching as follows: first, the dataset D was split into two halves A and B. Each of the n attributes
2
Note that corresponding attributes may have different distributions in real-world databases. Hence, schema
matching cannot solely rely on distribution testing. Advanced approaches to schema matching using MMD as
one key statistical test are a topic of current research.
in A (and B, resp.) was then represented by its instances in A (resp. B). We then tested all pairs
of attributes from A and from B against each other, to find the optimal assignment of attributes
A1 , . . . , An from A to attributes B1 , . . . , Bn from B. We assumed that A and B contain the same
number of attributes.
As a naive approach, one could assume that any possible pair of attributes might correspond, and
thus that every attribute of A needs to be tested against all the attributes of B to find the optimal
match. We report results for this naive approach, aggregated over all pairs of possible attribute
matches, in Table 2. We used three datasets: the census income dataset from the UCI KDD archive
(CNUM), the protein homology dataset from the 2004 KDD Cup (BIO) [8], and the forest dataset
from the UCI ML archive [5]. For the final dataset, we performed univariate matching of attributes
(FOREST) and multivariate matching of tables (FOREST10D) from two different databases, where
each table represents one type of forest. Both our asymptotic MMD2u -based tests perform as well as
or better than the alternatives, notably for CNUM, where the advantage of MMD2u is large. Unlike
in Table 1, the next best alternatives are not consistently the same across all data: e.g. in BIO they
are Wolf or Hall, whereas in FOREST they are Smir, Biau, or the t-test. Thus, MMD2u appears to
perform more consistently across the multiple datasets. The Friedman-Rafsky tests do not always
return a Type I error close to the design parameter: for instance, Wolf has a Type I error of 9.7% on
the BIO dataset (on these data, MMD2u has the joint best Type II error without compromising the
designed Type I performance). Finally, our uniform convergence approach performs much better
than in Table 1, although surprisingly it fails to detect differences in FOREST10D.
A more principled approach to attribute matching is also possible. Assume that φ(A) =
(φ1 (A1 ), φ2 (A2 ), ..., φn (An )): in other words, the kernel decomposes into kernels on the individual
attributes
A (and also decomposes this way on the attributes of B). In this case, M M D2 can be
Pof
n
written i=1 kµi (Ai ) − µi (Bi )k2 , where we sum over the MMD terms on each of the attributes.
Our goal of optimally assigning attributes from B to attributes of
PA via MMD is equivalent to finding the optimal permutation π of attributes of B that minimizes ni=1 kµi (Ai ) − µi (Bπ(i) )k2 . If we
define Cij = kµi (Ai ) − µi (Bj )k2 , then this is the same as minimizing the sum over Ci,π(i) . This is
the linear assignment problem, which costs O(n3 ) time using the Hungarian method [19].
Dataset
BIO
FOREST
CNUM
FOREST10D
Attr.
Same
Different
Same
Different
Same
Different
Same
Different
MMD
100.0
20.0
100.0
4.9
100.0
15.2
100.0
100.0
MMD2u B
93.8
17.2
96.4
0.0
94.5
2.7
94.0
0.0
MMD2u M
94.8
17.6
96.0
0.0
93.8
2.5
94.0
0.0
t-test
95.2
36.2
97.4
0.2
94.0
19.17
100.0
0.0
Wolf
90.3
17.2
94.6
3.8
98.4
22.5
93.5
0.0
Smir
95.8
18.6
99.8
0.0
97.5
11.6
96.5
1.0
Hall
95.3
17.9
95.5
50.1
91.2
79.1
97.0
72.0
Biau
99.3
42.1
100.0
0.0
98.5
50.5
100.0
100.0
Table 2: Naive attribute matching on univariate (BIO, FOREST, CNUM) and multivariate data
(FOREST10D). Numbers indicate the percentage of accepted null hypothesis (p=q) pooled over
attributes. α = 0.05. Sample size (dimension; attributes; repetitions of experiment): BIO 377 (1; 6;
100); FOREST 538 (1; 10; 100); CNUM 386 (1; 13; 100); FOREST10D 1000 (10; 2; 100).
We tested this ’Hungarian approach’ to attribute matching via MMD2u B on three univariate datasets
(BIO, CNUM, FOREST) and for table matching on a fourth (FOREST10D). To study MMD2u B
on structured data, we obtained two datasets of protein graphs (PROTEINS and ENZYMES) and
used the graph kernel for proteins from [7] for table matching via the Hungarian method (the other
tests were not applicable to this graph data). The challenge here is to match tables representing
one functional class of proteins (or enzymes) from dataset A to the corresponding tables (functional
classes) in B. Results are shown in Table 3. Besides on the BIO dataset, MMD2u B made no errors.
6 Summary and Discussion
We have established two simple multivariate tests for comparing two distributions p and q. The test
statistics are based on the maximum deviation of the expectation of a function evaluated on each
of the random variables, taken over a sufficiently rich function class. We do not require density
Dataset
BIO
CNUM
FOREST
FOREST10D
ENZYME
PROTEINS
Data type
univariate
univariate
univariate
multivariate
structured
structured
No. attributes
6
13
10
2
6
2
Sample size
377
386
538
1000
50
200
Repetitions
100
100
100
100
50
50
% correct matches
90.0
99.8
100.0
100.0
100.0
100.0
Table 3: Hungarian Method for attribute matching via MMD2u B on univariate (BIO, CNUM, FOREST), multivariate (FOREST10D), and structured data (ENZYMES, PROTEINS) (α = 0.05; ‘%
correct matches’ is the percentage of the correct attribute matches detected over all repetitions).
estimates as an intermediate step. Our method either outperforms competing methods, or is close to
the best performing alternative. Finally, our test was successfully used to compare distributions on
graphs, for which it is currently the only option.
Acknowledgements: The authors thank Matthias Hein for helpful discussions, Patrick Warnat
(DKFZ, Heidelberg) for providing the microarray datasets, and Nikos Logothetis for providing the
neural datasets. NICTA is funded through the Australian Government’s Backing Australia’s Ability
initiative, in part through the ARC. This work was supported in part by the IST Programme of the
European Community, under the PASCAL Network of Excellence, IST-2002-506778.
References
[1] N. Anderson, P. Hall, and D. Titterington. Two-sample test statistics for measuring discrepancies between two multivariate probability density functions using kernel-based density estimates. Journal of
Multivariate Analysis, 50:41–54, 1994.
[2] M. Arcones and E. Gin´e. On the bootstrap of u and v statistics. The Annals of Statistics, 20(2):655–674,
1992.
[3] G. Biau and L. Gyorfi. On the asymptotic properties of a nonparametric l1 -test statistic of homogeneity.
IEEE Transactions on Information Theory, 51(11):3965–3973, 2005.
[4] P. Bickel. A distribution free version of the Smirnov two sample test in the p-variate case. The Annals of
Mathematical Statistics, 40(1):1–23, 1969.
[5] C. L. Blake and C. J. Merz. UCI repository of machine learning databases, 1998.
[6] K. M. Borgwardt, A. Gretton, M.J. Rasch, H.P. Kriegel, B. Sch¨olkopf, and A.J. Smola. Integrating
structured biological data by kernel maximum mean discrepancy. In ISMB, 2006.
[7] K. M. Borgwardt, C. S. Ong, S. Schonauer, S. V. N. Vishwanathan, A. J. Smola, and H. P. Kriegel. Protein
function prediction via graph kernels. Bioinformatics, 21(Suppl 1):i47–i56, Jun 2005.
[8] R. Caruana and T. Joachims. Kdd cup. http://kodiak.cs.cornell.edu/kddcup/index.html, 2004.
[9] G. Casella and R. Berger. Statistical Inference. Duxbury, Pacific Grove, CA, 2nd edition, 2002.
[10] R. M. Dudley. Real analysis and probability. Cambridge University Press, Cambridge, UK, 2002.
[11] R. Fortet and E. Mourier. Convergence de la r´eparation empirique vers la r´eparation th´eorique. Ann.
´
Scient. Ecole
Norm. Sup., 70:266–285, 1953.
[12] J. Friedman and L. Rafsky. Multivariate generalizations of the Wald-Wolfowitz and Smirnov two-sample
tests. The Annals of Statistics, 7(4):697–717, 1979.
[13] A. Gretton, K. Borgwardt, M. Rasch, B. Sch¨olkopf, and A. Smola. A kernel method for the two sample
problem. Technical Report 157, MPI for Biological Cybernetics, 2007.
[14] G. R. Grimmet and D. R. Stirzaker. Probability and Random Processes. Oxford University Press, Oxford,
third edition, 2001.
[15] P. Hall and N. Tajvidi. Permutation tests for equality of distributions in high-dimensional settings.
Biometrika, 89(2):359–374, 2002.
[16] M. Hein, T.N. Lal, and O. Bousquet. Hilbertian metrics on probability measures and their application in
svm’s. In Proceedings of the 26th DAGM Symposium, pages 270–277, Berlin, 2004. Springer.
[17] N. Henze and M. Penrose. On the multivariate runs test. The Annals of Statistics, 27(1):290–298, 1999.
[18] N. L. Johnson, S. Kotz, and N. Balakrishnan. Continuous Univariate Distributions. Volume 1 (Second
Edition). John Wiley and Sons, 1994.
[19] H.W. Kuhn. The Hungarian method for the assignment problem. Naval Research Logistics Quarterly,
2:83–97, 1955.
[20] P. Rosenbaum. An exact distribution-free test comparing two multivariate distributions based on adjacency. Journal of the Royal Statistical Society B, 67(4):515–530, 2005.
[21] R. Serfling. Approximation Theorems of Mathematical Statistics. Wiley, New York, 1980.
[22] I. Steinwart. On the influence of the kernel on the consistency of support vector machines. Journal of
Machine Learning Research, 2:67–93, 2002.